If your client-side config and the server-side config are different, you can't join the server because the mod removes the entries for those blocks.

Extremely noticeable with Bubble Columns and Sea Grass being disabled / enabled.

I would strongly advise that you don't try changing settings at runtime; there are a lot of things that are very likely to go wrong if you do that.

This is intended behavior; you should keep the configs synchronized unless you have a very good reason not to.

I can't really control other people's configs, bubble columns are disabled by default.

Unfortunately, the way Forge works, you will have to supply them a config file (e.g. as part of a modpack). Even if I wanted to support server->client synchronization, I am not sure I can take blocks in and out of the registry at runtime.

Oh, toggling the option for Bubble Columns works without restarting the game, I had to test it, it might even work without leaving the world, though it acted kind of buggy when I did that.

It seemed to work fine.. you could test it yourself if you're curious

Interesting. If it works for you that's good, but I don't understand why or how it does work. 😆 In any case, I'm going to close this as the original report is not a bug.